Package index • bambamR

Data Import

Read FASTQ and BAM files into R.

bb_read_fastq(): Read FASTQ Files
bb_read_bam(): Read BAM Files
bb_count_bam(): Count Reads in BAM File

Quality Control

Compute and visualize QC metrics from sequencing data.

bb_qc(): Generate QC Metrics
bb_qc_summary(): QC Summary
bb_plot_qc(): QC Visualization Panel

Alignment & Counting

Align reads to a reference genome and count per-gene overlaps.

bb_align(): Align Reads to Reference Genome
bb_count_reads(): Count Reads per Gene/Feature

Normalization

Normalize raw count matrices (CPM, TPM, TMM, RLE).

bb_normalize(): Normalize Count Matrix

Differential Expression

Wrappers for DESeq2, edgeR, and limma-voom that return standardized results.

bb_deseq2(): Differential Expression with DESeq2
bb_edger(): Differential Expression with edgeR
bb_limma_voom(): Differential Expression with limma-voom

Visualization

Publication-ready plots. Every function returns a ggplot2 object.

bb_oncoplot(): Create Publication-Ready Oncoplot
bb_volcano(): Volcano Plot
bb_heatmap(): Heatmap of Top Differentially Expressed Genes
bb_pca(): PCA Plot
bb_ma_plot(): MA Plot

Pipeline & Export

Run the full end-to-end pipeline and export results.

bb_pipeline(): Run Full bambamR Pipeline
bb_export_rds(): Export Results to RDS
bb_export_csv(): Export DE Results to CSV
bb_export_tsv(): Export DE Results to TSV
bb_run_app(): Launch bambamR Shiny App

Example Data

Bundled datasets for exploring every feature without external files.

bb_example_counts(): Load Example Count Matrix
bb_example_mutations(): Load Example Mutation Data
bb_example_de(): Load Example DE Results

Classes & Methods

S3 classes for pipeline results and QC objects.

print(<bb_result>): Print method for bb_result
print(<bb_qc>): Print method for bb_qc
summary(<bb_qc>): Summary method for bb_qc
bambamR bambamR-package: bambamR: End-to-End RNA-Seq Processing from FASTQ to Publication-Ready Plots